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145 results for “trichomes”
Small RNA-seq data from leaf, stem trichomes, bald stems and leaf primordiums from different tomato genetic backgrounds
<p><strong>Description</strong></p> <p>Various tissues of cultivated and wild tomato genotypes were harvested.</p> <p>Trichomes are stem trichomes (isolated from the stem of tomatoes).</p> <p><strong>RNA isolation</strong></p> <p>To isolate RNA, plant tissues were flash frozen in liquid nitrogen immediately after harvesting and stored at −80°C prior to RNA extraction. Frozen pellets were grounded by using a mortar and pestle before immersion in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified into two separate fractions (>200 nt and <200 nt) using the miRNeasy Mini kit (Qiagen). For the >200 nt RNA an on-column treatment was included using the RNase-free DNase set (Qiagen).</p> <p><strong>Small RNA-Seq</strong></p> <p>Small RNA-Seq libraries were generated from the <200 nt RNA fraction according to the manufacturers’ protocols using the Small RNA-Seq Library Prep Kit (Lexogen). The size distribution of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The libraries were quantified on a QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to the instructions of the manufacturer. The libraries were clustered and sequenced (75 bp) on a NextSeq 550 Sequencing System (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina).</p> <p> </p> <p><strong>The list of samples</strong> is available in the <a href="https://zenodo.org/api/files/195143fa-2210-4b7f-bfe2-a649e124b7b0/sample_list.csv">sample_list.csv</a> file.</p> <ul> <li>Myc-1 stands for a knock-out mutant of the MYC1 gene (Solyc08g005050). The line full name is MS5-4.</li> <li>Pik is an introgression line containing a fragment of chromosome 1 from <em>S. habrochaites</em> PI127826 into a MicroTom genetic background. </li> </ul> <p> </p> <p><strong>Pooled samples</strong></p> <p>Some samples corresponding to the same tomato genotype and tissue were pooled altogether and are also available in fastq format.</p> <pre><code class="language-markdown">| species | genotype | pool_of | tissue | file | reads | |--------------|------------|---------------|----------------|----------|----------| | habrochaites | PI127826 | S01, S02, S03 | trichomes | PI127826.fastq.gz | 16,539,495 | | lycopersicum | Moneymaker | S04, S05, S06 | trichomes | Moneymaker.fastq.gz | 11,539,748 | | habrochaites | LYC4 | S07, S08, S25 | trichomes | LYC4.fastq.gz | 15,980,718 | | lycopersicum | LA4024 | S10, S11, S12 | trichomes | LA4024.fastq.gz | 13,888,953 | | habrochaites | LA1777 | S13, S14, S15 | trichomes | LA1777.fastq.gz | 14,136,265 | | pennellii | LA0716 | S19, S20, S21 | trichomes | LA0716.fastq.gz | 14,045,182 |</code></pre> <p> </p>
Messenger RNA-seq data from leaves, stem trichomes, bald stems and leaf primordia from different tomato genetic backgrounds
<p><strong>RNA isolation</strong></p> <p>To isolate RNA, plant tissues were flash frozen in liquid nitrogen immediately after harvesting and stored at −80°C prior to RNA extraction. Frozen pellets were grounded by using a mortar and pestle before immersion in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified into two separate fractions (>200 nt and <200 nt) using the miRNeasy Mini kit (Qiagen). For the >200 nt RNA an on-column treatment was included using the RNase-free DNase set (Qiagen).</p> <p><strong>mRNA sequencing protocol</strong></p> <p>A poly-A enrichment was performed on the >200 nt RNA fraction using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). RNA-Seq libraries were generated according to the manufacturers’ protocols using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) (New England BioLabs). The size distribution of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The libraries were quantified on a QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to the instructions of the manufacturer. The libraries were clustered and sequenced (75 bp) on a NextSeq 550 Sequencing System (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina).</p> <p><strong>List of samples is available in the <a href="https://zenodo.org/api/files/168d9731-fc3e-4baa-8053-1656862769ee/mrna_sample_list.csv?versionId=de4bd2de-7ddc-4d03-9ac6-545f98896874">mrna_sample_list.csv</a> file.</strong></p> <ul> <li>Myc-1 stands for a knock-out mutant of the MYC1 gene (Solyc08g005050). The line full name is MS5-4.</li> </ul> <p> </p> <p><strong>Processed data</strong></p> <ul> <li><strong>Samples S28 to S48 </strong> <ul> <li>Provenance: run from the snakemake_rnaseq pipeline v0.3.1 available from <a href="https://github.com/BleekerLab/snakemake_rnaseq/releases/tag/v0.3.1">GitHub</a> and <a href="http:// https://zenodo.org/record/4034215">Zenodo</a>:</li> <li><strong>Scaled counts:</strong> `S28_to_S48_scaled_counts.tsv<strong>`. </strong>A file with DESeq2 normalised counts wiith tab-separated values. Useful for visualisations (heatmaps, PCA) <em>NOT</em> for differential expression analysis. </li> <li><strong>Raw counts:</strong> `S28_to_S48_raw_counts.tsv<strong>`. </strong>A file with the raw counts that can be used for differential expression analysis with DESeq2. </li> </ul> </li> </ul> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Solanum section Lycopersicon (cultivated and wild tomato genotypes) trichome pictures
<p><strong>Stem trichome pictures of various genotypes from the <em>Solanum</em> section Lycopersicon:</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401 | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p><strong>Pictures were taken in March 2018 following this two-step protocol:</strong></p> <pre><code class="language-markdown"># Making high-quality pictures of tomato trichomes This protocol is to take high-quality pictures of trichomes and stack them into one unique final picture. The stem from the 4th leaf from the top will be used to make a picture. This protocol is composed of two parts: - Firstly: take a series of pictures (15 to 30 pictures) using a stereomicroscope - Secondly: photo stacking using Photoshop # First part: taking pictures using the Leica MZFLII 1. Turn on the microscope zoom mechanism 2. Turn on the ebq 100 lamp and the Olympus Highlight 2000 lamp 3. Make sure no filter (e.g. dsRed) is applied 4. Open the Nikon NIS-Elements program. 5. Take a piece of stem and place it horizontally (---) under the microscope. . 6. Zoom out completely. 7. Zoom in at 10,000x on the side of the branch ("labeled 10.0 on the microscope). 8. Focus on a few trichomes. Get them as much as possible in focus. This is going to be your first picture (foreground). 9. Zoom in about a few trichome layers away. There should not be too much overlap between the different trichomes (otherwise they get merged together during the stacking phase). This will be your background. 10. Zoom out to go back to the foreground (= your first picture). 11. Depending on the number of trichomes in-between your foreground and background, you need to take a variable number of pictures. - If trichome density is high, then trichomes will overlap during the stacking meaning that you need to take more pictures (~30) and reduce the distance between your foreground and background. - If trichome density is low, then trichomes won't overlap and you need less pictures (~10) # Second part: alignment of pictures using Photoshop See the trichome layer photography protocol (PDF file)made by Maurice Heilijgers (August 2018).</code></pre> <p> </p>
Detection and Quantification of Cotton Trichomes by Deep Learning Algorithm
<p>This file includes three image datasets for singled and clustered trichomes: the original image dataset, the black-and-white image dataset, and the enhanced image dataset. In addition, the codes of the four models are included. The details are in the article "Detection and Quantification of Cotton Trichomes by Deep Learning Algorithm".</p>
Stem trichome PARE-Seq (degradome) data from the 20 accessions
<p><strong>PARE-Seq / degradome dataset</strong></p> <p>Obtained from 10µg of total RNA isolated from stem trichomes of cultivated (S. lycopersicum) and wild relatives of tomato (Solanum section Lycopersicon). </p> <p>Degradome sequencing (sequencing of 5' end of uncapped mRNAs --> to find the site of microRNA cleavage).<br> Degradome sequencing is also called PARE-Seq (see German et al., Nature Protocols 2009 4(3):356-62). Here, Vertis Biotech AG used a slightly modified protocol that generates 75nt reads from the 5' uncapped end of the mRNA. </p> <p><strong>Sample description</strong><br> Stem trichomes total RNA from several individual plants of the "20 accessions" (see table of genotypes below). See lab book - Marc Galland lab book #4 (2017): pages 61-69 + 73-75.</p> <p><strong>Protocol used</strong><br> Qiagen RNeasy Plant Mini Kit (Cat No./ID: 74904).<br> DNAse treatment by Vertis. <br> Minimal amount of 10µg of total RNA per sample.</p> <p><strong>Sequencing at Vertis Biotech AG (Germany)</strong><br> See Doc_VB1745_Galland.pdf and Doc_VB1745_2_Galland.pdf together with the two SeqData08.08.2017.pdf and SeqData08.</p> <p>The sequencing run has generated a total of 20 fastq files: </p> <ol> <li>Moneymaker_C32_S3_R1_001.fastqc.gz</li> <li>LA0407_S10_R1_001.fastq.gz</li> <li>LA0716_S29_R1_001.fastq.gz</li> <li>LA1278_S27_R1_001.fastq.gz</li> <li>LA1364_S8_R1_001.fastq.gz</li> <li>LA1401_S5_R1_001.fastq.gz</li> <li>LA1578_S26_R1_001.fastq.gz</li> <li>LA1718_S4_R1_001.fastq.gz</li> <li>LA1777_S7_R1_001.fastq.gz</li> <li>LA1840_S6_R1_001.fastq.gz</li> <li>LA1954_S28_R1_001.fastq.gz</li> <li>LA2133_S9_R1_001.fastq.gz</li> <li>LA2172_S11_R1_001.fastq.gz</li> <li>LA2386_S21_R1_001.fastq.gz</li> <li>LA2695_S20_R1_001.fastq.gz</li> <li>LA4024_S26_R1_001.fastq.gz</li> <li>LA0735_LYC140_S24_R1_001.fastq.gz</li> <li>PI134418_LYC38_S23_R1_001.fastq.gz</li> <li>LYC4_S25_R1_001.fastq.gz</li> <li>PI127826_S22_R1_001.fastq.gz</li> </ol> <p><strong>Table of genotypes used</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p> </p> <p><strong>Reference:</strong></p> <p>German et al., Nature Protocols 2009 4(3):356-62)</p>
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